feat: enable config of node-specific fields in vlm response (Issue #27)

.env.example

@@ -0,0 +1,7 @@
+###########################
+## VLM RESPONSE SETTINGS ##
+###########################
+HANDOVER_TYPE_ID="GREGoR-NCH"
+HANDOVER_TYPE_LABEL="GREGoR AnyVLM Reference"
+BEACON_HANDOVER_URL="https://variants.gregorconsortium.org/"
+BEACON_NODE_ID="org.anyvlm.gregor"

.github/workflows/python-package.yaml

@@ -47,6 +47,10 @@ jobs:
         run: uv run pytest
         env:
           ANYVLM_ANYVAR_TEST_STORAGE_URI: postgresql://postgres:postgres@localhost:5432/postgres
+          HANDOVER_TYPE_ID: GREGoR-NCH
+          HANDOVER_TYPE_LABEL: "GREGoR AnyVLM Reference"
+          BEACON_HANDOVER_URL: https://variants.gregorconsortium.org/
+          BEACON_NODE_ID: org.anyvlm.gregor
   lint:
     name: lint
     runs-on: ubuntu-latest

src/anyvlm/schemas/vlm.py

@@ -1,36 +1,62 @@
 """Schemas relating to VLM API."""
 
+import os
 from typing import ClassVar, Literal, Self
 
 from pydantic import BaseModel, ConfigDict, Field, model_validator
 
 from anyvlm.utils.types import Zygosity
 
-# ruff: noqa: N815 (allows camelCase vars instead of snake_case to align with expected VLM protocol response)
+# ruff: noqa: N815, N803, D107 (allow camelCase instead of snake_case to align with expected VLM protocol response + don't require init docstrings)
 
 RESULT_ENTITY_TYPE = "genomicVariant"
 
 
+class MissingEnvironmentVariableError(Exception):
+    """Raised when a required environment variable is not set."""
+
+
+def _get_environment_var(key: str) -> str:
+    value: str | None = os.environ.get(key)
+    if not value:
+        message = f"Missing required environment variable: {key}"
+        raise MissingEnvironmentVariableError(message)
+    return value
+
+
 class HandoverType(BaseModel):
     """The type of handover the parent `BeaconHandover` represents."""
 
     id: str = Field(
-        default="gregor", description="Node-specific identifier"
-    )  # TODO: enable configuration of this field. See Issue #27.
+        default_factory=lambda: _get_environment_var("HANDOVER_TYPE_ID"),
+        description="Node-specific identifier",
+    )
     label: str = Field(
-        default="GREGoR AnVIL browser", description="Node-specific label"
-    )  # TODO: enable configuration of this field. See Issue #27.
+        default_factory=lambda: _get_environment_var("HANDOVER_TYPE_LABEL"),
+        description="Node-specific label",
+    )
+
+    # custom __init__ to prevent overriding attributes that are set via environment variables
+    def __init__(self) -> None:
+        super().__init__()
 
 
 class BeaconHandover(BaseModel):
     """Describes how users can get more information about the results provided in the parent `VlmResponse`"""
 
-    handoverType: HandoverType = HandoverType()
+    handoverType: HandoverType = Field(default=HandoverType())
     url: str = Field(
-        default="https://anvil.terra.bio/#workspaces?filter=GREGoR",  # TODO: enable configuration of this field. See Issue #27.
-        description="A url which directs users to more detailed information about the results tabulated by the API (ideally human-readable)",
+        default_factory=lambda: _get_environment_var("BEACON_HANDOVER_URL"),
+        description="""
+            A url which directs users to more detailed information about the results tabulated by the API. Must be human-readable.
+            Ideally links directly to the variant specified in the query, but can be a generic search page if necessary.
+        """,
     )
 
+    # custom __init__ to prevent overriding attributes that are static/set via environment variables
+    def __init__(self) -> None:
+        super().__init__()
+
 
 class ReturnedSchema(BaseModel):
     """Fixed [Beacon Schema](https://github.com/ga4gh-beacon/beacon-v2/blob/c6558bf2e6494df3905f7b2df66e903dfe509500/framework/json/common/beaconCommonComponents.json#L241)"""
@@ -42,7 +68,7 @@ class ReturnedSchema(BaseModel):
     schema_: str = Field(
         default="ga4gh-beacon-variant-v2.0.0",
         # Alias is required because 'schema' is reserved by Pydantic's BaseModel class,
-        # But VLM expects a field named 'schema'
+        # But VLM protocol expects a field named 'schema'
         alias="schema",
     )
 
@@ -57,7 +83,7 @@ class Meta(BaseModel):
         description="The version of the VLM API that this response conforms to",
     )
     beaconId: str = Field(
-        default="org.gregor.beacon",  # TODO: enable configuration of this field. See Issue #27.
+        default_factory=lambda: _get_environment_var("BEACON_NODE_ID"),
         description="""
             The Id of a Beacon. Usually a reversed domain string, but any URI is acceptable. The purpose of this attribute is,
             in the context of a Beacon network, to disambiguate responses coming from different Beacons. See the beacon documentation
@@ -66,6 +92,10 @@ class Meta(BaseModel):
     )
     returnedSchemas: list[ReturnedSchema] = [ReturnedSchema()]
 
+    # custom __init__ to prevent overriding attributes that are static or set via environment variables
+    def __init__(self) -> None:
+        super().__init__()
+
 
 class ResponseSummary(BaseModel):
     """A high-level summary of the results provided in the parent `VlmResponse"""
@@ -104,6 +134,10 @@ class ResultSet(BaseModel):
         description=f"The type of entity relevant to these results. Must always be set to '{RESULT_ENTITY_TYPE}'",
     )
 
+    # custom __init__ to prevent inadvertently overriding static fields
+    def __init__(self, resultset_id: str, resultsCount: int) -> None:
+        super().__init__(id=resultset_id, resultsCount=resultsCount)
+
 
 class ResponseField(BaseModel):
     """A list of ResultSets"""

tests/conftest.py

@@ -6,14 +6,7 @@
 from ga4gh.vrs import models
 from pydantic import BaseModel
 
-
-@pytest.fixture(scope="session", autouse=True)
-def load_env():
-    """Load `.env` file.
-
-    Must set `autouse=True` to run before other fixtures or test cases.
-    """
-    load_dotenv()
+load_dotenv()
 
 
 @pytest.fixture(scope="session")

tests/unit/test_schemas.py

@@ -5,7 +5,6 @@
 import pytest
 
 from anyvlm.schemas.vlm import (
-    RESULT_ENTITY_TYPE,
     HandoverType,
     ResponseField,
     ResponseSummary,
@@ -31,30 +30,24 @@ def responses_with_invalid_resultset_ids(valid_handover_id) -> list[ResponseFiel
         ResponseField(
             resultSets=[
                 ResultSet(
-                    exists=True,
                     id=f"invalid_handover_id {Zygosity.HOMOZYGOUS}",
                     resultsCount=0,
-                    setType=RESULT_ENTITY_TYPE,
                 )
             ]
         ),
         ResponseField(
             resultSets=[
                 ResultSet(
-                    exists=True,
                     id=f"{valid_handover_id} invalid_zygosity",
                     resultsCount=0,
-                    setType=RESULT_ENTITY_TYPE,
                 )
             ]
         ),
         ResponseField(
             resultSets=[
                 ResultSet(
-                    exists=True,
                     id=f"{Zygosity.HOMOZYGOUS}-{valid_handover_id}",  # incorrect order/formatting
                     resultsCount=0,
-                    setType=RESULT_ENTITY_TYPE,
                 )
             ]
         ),
@@ -65,10 +58,8 @@ def test_valid_resultset_id(response_summary, valid_handover_id):
     response = ResponseField(
         resultSets=[
             ResultSet(
-                exists=True,
                 id=f"{valid_handover_id} {Zygosity.HOMOZYGOUS}",
                 resultsCount=0,
-                setType=RESULT_ENTITY_TYPE,
             )
         ]
     )